Get the screws right too.
I had the same problem and used poly-sulfide with great success so far (3 years). The key, I believe, was getting all the screws to hold. In my first attempt I used silicon and did not get all the screws to hold as some where stripped out. Well it lasted no time at all as the water hose test demonstrated when the silicon had set. I took the panel out and drilled out the holes, filled then with thickened epoxy and re drilled them for the screws. Having a mechanical bond and not using silicon (it does not have the adhesive properties of poly) was the trick for me.Also the Plexiglas panel is 3/8" which is not normally available at home depot. I had to order it on line. If I had to do it again I'd spend the extra bucks on lextan as I am now seeing glazing cracks (the panel is curved about 3" in a 36" run). Seems I can't get the admiral and kids to not step on it when messing around the mast.